\index{general}{jack2hen|see{clades}}
\index{poy3}{agree|see{constraint}}
\index{poy3}{bremer|see{calculatesupports}}
\index{poy3}{bremerspr|see{calculatesupports, swap}}
\index{poy3}{build|see{build}}
\index{poy3}{topodiagnoseonly|see{read}}
\index{poy3}{buildmaxtrees|see{trees}}
\index{poy3}{buildslop|see{threshold}}
\index{poy3}{buildspr|see{spr}}
\index{poy3}{buildtbr|see{tbr}}
\index{poy3}{characterweights|see{report}}
\index{poy3}{commandfile|see{run}}
\index{poy3}{commandfiledir|see{cd}}
\index{poy3}{datadir|see{cd}}
\index{poy3}{defaultweight|see{weight}}
\index{poy3}{diagnose|see{report}}
\index{poy3}{disagree|see{constraint}}
\index{poy3}{driftequallaccept|see{drifting}}
\index{poy3}{driftlengthbase|see{drifting}}
\index{poy3}{driftspr|see{drifting}}
\index{poy3}{drifttbr|see{drifting}}
\index{poy3}{drifttrees|see{drifting}}
\index{poy3}{dropconstraints|see{constraint}}
\index{poy3}{extensiongap|see{gapopening}}
\index{poy3}{extensiongap|see{tcm}}
\index{poy3}{gap|see{tcm}}
\index{poy3}{gap|see{gapopening}}
\index{poy3}{gc|see{memory}}
\index{poy3}{holdmaxtrees|see{trees}}
\index{poy3}{hypancfile|see{diagnosis}}
\index{poy3}{hypancname|see{diagnosis}}
\index{poy3}{impliedalignment|see{implied\_alignment}}
\index{poy3}{iafiles|see{implied\_alignment}}
\index{poy3}{noiafiles|see{report}}
\index{poy3}{indices|see{treestats}}
\index{poy3}{intermediate|see{trajectory}}
\index{poy3}{jackboot|see{jackknife}}
\index{poy3}{jackfrequencies|see{jackknife}}
\index{poy3}{jackoutgroup|see{outgroup}}
\index{poy3}{jackstart|see{jackknife}}
\index{poy3}{poytreefile|see{trees}}
\index{poy3}{poybintreefile|see{trees}}
\index{poy3}{poystrictconsensustreefile|see{consensus}}
\index{poy3}{leading|see{trailing\_insertion}}
\index{poy3}{maxtrees|see{trees}}
\index{poy3}{molecularmatrix|see{tcm}}
\index{poy3}{newstates|see{fixed\_states}}
\index{poy3}{numdriftchanges|see{repeat}}
\index{poy3}{numdriftspr|see{repeat}}
\index{poy3}{numdrifttbr|see{repeat}}
\index{poy3}{phastwincladfile|see{phastwinclad}}
\index{poy3}{plotfile|see{graphtrees}}
\index{poy3}{plotfrequencies|see{graphtrees}}
\index{poy3}{plotechocommandline|see{echo}}
\index{poy3}{plotmajority|see{graphconsensus}}
\index{poy3}{plotoutgroup|see{outgroup}}
\index{poy3}{plotstrict|see{graphconsensus}}
\index{poy3}{plottrees|see{graphtrees}}
\index{poy3}{printtree|see{asciitrees}}
\index{poy3}{random|see{trees}}
\index{poy3}{replicates|see{trees}}
\index{poy3}{ratchetoverpercent|see{ratchet}}
\index{poy3}{ratchetpercent|see{ratchet}}
\index{poy3}{ratchetseverity|see{ratchet}}
\index{poy3}{ratchetslop|see{perturb}}
\index{poy3}{ratchetspr|see{perturb}}
\index{poy3}{ratchettbr|see{perturb}}
\index{poy3}{ratchettrees|see{perturb}}
\index{poy3}{ratchetinseq|see{perturb}}
\index{poy3}{slop|see{threshold}}
\index{poy3}{sprmaxtrees|see{trees}}
\index{poy3}{staticapprox|see{static\_approx}}
\index{poy3}{staticapproxbuild|see{build}}
\index{poy3}{tbrmaxtrees|see{trees}}
\index{poy3}{topofile|see{read}}
\index{poy3}{topology|see{read}}
\index{poy3}{topolist|see{trees}}
\index{poy3}{topooutgroup|see{outgroup}}
\index{poy3}{treefuse|see{fuse}}
\index{poy3}{treefusespr|see{fuse}}
\index{poy3}{treefusetbr|see{fuse}}
\index{poy3}{cat\_commandbrowsing|see{help}}
\index{poy3}{cat\_helptopics|see{help}}
\index{poy3}{replicatebuild|see{trees}}
\index{poy3}{replicaterefinement|see{trees}}
\index{poy3}{finalrefinement|see{swap}}
\index{poy3}{trailinggap|see{trailinginsertion}}
\index{poy3}{trailinggap|see{trailingdeletion}}
% --
% -2n2reorder
% -allchroms
% -alltrees
% -approxbuild
% -approxdrift
% -approxquickspr
% -approxquicktbr
% -basefreq
% -cmptreefilefile
% -cmp2treefiles
% -cmp1treefile
% -bayes
% -bayesroundup
% -buildchrom
% -catchfile
% -catchslaveoutput
% -change
% -checkfrequency
% -checkslop
% -chromegap
% -chromelocusgap
% -chromesizegap
% -chromfilter
% -chromosome
% -circular
% -crashslave
% -crashcontroller
% -crashreserve
% -compressstates
% -controllers
% -cutswap
% -discrepancies
% -distcost
% -dogaptie
% -enabletmpfiles
% -estimateparamsfirst
% -estimatep
% -estimateq
% -exact
% -onversionconflict
% -fitchtrees
% -freqmodel
% -fuselimit
% -fusemaxtrees
% -minterminals
% -fusemingroup
% -fusingrounds
% -gammaalpha
% -gammaclasses
% -genome
% -getnewmatrix
% -goloboff
% -horizontalcost
% -horizontalrecombination
% -horizontalsizecost
% -horizontaltranslocationcost
% -incremental
% -insertpipes
% -invdist
% -invariantsitesadjust
% -iterativeinitfinal
% -iterativeinitsingle
% -iterativekeepbetter
% -iterativelowmem
% -iterativepass
% -iterativepassfinal
% -iterativerandom
% -jackexclusion
% -jackcharfile
% -jacktree
% -jackpseudotrees
% -jackpseudoconsensustrees
% -jackftree
% -jackfpseudotrees
% -jackfpseudoconsensustrees
% -jackwincladfile
% -poystrictconsensuscharfile
% -poymctreefile
% -poymccharfile
% -mrcutoff
% -mrcutpoymctreefile
% -mrcutpoymccharfile
% -mrcutplotmajority
% -mrcutplotfrequencies
% -topocutoff
% -mrcutjacktree
% -mrcutjackftree
% -mrcutjackcharfile
% -mrcutjackfrequencies
% -jobspernode
% -mtx_partition
% -kbasefreq
% -kencoding
% -keventfreq
% -kmdl
% -kfile
% -kmod
% -kp
% -kmatrix
% -kunit
% -kfactor
% -likelihood
% -likelihoodconvergancevalue
% -likelihoodestimationsize
% -likelihoodesttranseachtime
% -likelihoodextensiongap
% -likelihoodmaxnumiterations
% -likelihoodnoncodinggap
% -likelihoodroundingmultiplier
% -likelihoodstep
% -likelihoodstepinterval
% -likelihoodtrailinggap
% -linear
% -locusextgap
% -locussizegap
% -locusgap
% -locusswap
% -locusswap3d
% -lowmemthreshold
% -maxiterations
% -maxprocessors
% -numslaveprocesses
% -minstop
% -buildsperreplicate
% -multibuild
% -nomultibuild
% -multidrift
% -multiplier
% -multirandom
% -multiratchet
% -n2reorder
% -n2reorderorders
% -onan
% -onannum
% -dpmonannum
% -dpmsolospawn
% -onechroms
% -onereorder
% -oneasis
% -overwritedataprotection
% -overwriteprotection
% -pack_topology_rep
% -pairmatrix
% -parallel
% -plotencoding
% -plotwidth
% -prealigned
% -printhypanc
% -printlotshypanc
% -printqmat
% -fastashortname
% -nofastashortname
% -deletegapsfrominput
% -nodeletegapsfrominput
% -polyaddconverttorange
% -nopolyaddconverttorange
% -printccode
% -editnames
% -noprintccode
% -qmatrix
% -quick
% -quote
% -randomizeoutgroup
% -randomizeslaves
% -rearrange
% -recode
% -repintermediate
% -rerootafterbuild
% -reversible
% -showchromsearch
% -showiterative
% -slave
% -solospawn
% -somechroms
% -spewbinary
% -statematrix
% -statenumber
% -statetax
% -stats
% -stopat
% -submodel
% -theta
% -time
% -topopickrandom
% -topopwpickrandom
% -toposkipidentical
% -notoposkipidentical
% -totallikelihood
% -translocationcost
% -translocationsizecost
% -transpositioncost
% -transpositionsizecost
% -transrecombination
% -treeweightscale
% -trullytotallikelihood
% -unpack_binary
% -upincremental
% -verbose
% -noiafexcludeexcluded
